User:Tilman Schirmer/Sandbox 202

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C-di-GMP specific phosphodiesterases

YukI


YukI is a dimer with each protomer composed of an EAL domain (with TIM barrel fold), a long helical linker, and a PAS-like domain.

The active site is situated at the C-terminal end of the central β-barrel of the EAL domain. The residues of the active site (here shown with labels) are well conserved, including E33 and L35 of the EAL signature motif.

The c-di-GMP substrate is bound flat upon the actve site with the divalent metal (here Ca++) being sandwiched between binding site and c-di-GMP.

BlrP1


BlrP1

BLUF domain

EAL domain

Active site global view

Active site with labels

Active site + ligand + Mn

Active site + ligand + Mn + HOH